I think a lot of things do get re-run a lot, but Cartoon Network seems to have a grudge against Mystery Incorporated for some reason.
Given how they've also treated Green Lantern
and Young Justice
, I suspect it's a matter of target demographics. CN and its advertisers want to appeal to younger viewers, and shows like those and SD:MI are more sophisticated and older-skewing. So they're just not getting the size or type of audience that the network and the advertisers are seeking.
Really, SD:MI was a Scooby-Doo series for people who don't like Scooby-Doo, such as myself -- so it follows that it might not appeal as much to people who are
fans of the more conventional Scooby franchise. Sure, there were elements of homage, but also a lot of revisionism and deconstruction, and the stories, despite mostly following the standard formula, tended to be darker and edgier. And especially this last batch of episodes got increasingly dark and strange, and departed further from the sort of thing most people looking for a show about Scooby-Doo would expect or want to see. Honestly, I can see why CN might've been uncomfortable with the darkness and scariness of those last few episodes.